What is it?

NSF definition from Goodman et al (Science 2016): Reproducibility refers to the ability of a researcher to duplicate the results of a prior study using the same materials as were used by the original investigator.

Do we agree?

Perhaps we should be talking about “Methods Reproducibility”

It is not the truth, or even an approximation of truth Reproducing the same bias/mistake = same (wrong) results

Reproducible Research

If most researchers think this is important,
why are we not working reproducibly?

What are the obstacles?

Think-Pair-Share
http://www.socrative.com
Student login, Room Name :AHREN

Fritiof Nilsson Piraten

Fritiof Nilsson Piraten

Translation

Procrastination

*I will add a picture for this later…

Procrastination

http://www.socrative.com
Student login, Room Name :AHREN

Fear

F: Fusion - Fusing the topic with bad thoughts about failure:
“I can not do this”
“It is too hard”
“It will take me too long time”

fEar

E: Excessive Goals - We get excited and want to change everything immediately
This leads to to unrealistic expectations and a high risk of failure!
Hard to keep up long term

feAr

A: Avoidance of Discomfort - All types of change will feel uncomfortable and unfamiliar at first
Avoiding discomfort, taking the easy way out (=no change)
Change is scary!

feaR

R: Remoteness from Values - Easy to loose goal and purpose
“Why am I even doing this?”

Can we overcome procrastination?

Note: Get organised! does not help!

How did the comments in Socrative fit with FEAR acronym?

My thoughts on Data management

• Acknowledge the procrastination psychology
  
• Set realistic goals but do set them
  
• A small step forward is progress!
  
• Set deadline
  
• Share and help each other & give positive feedback (e.g. github repo)

What will I try to cover

• Project and File structure
• File names
• Version control
• Dos & Don’ts

Possibly discuss (if time allows)

Project and File structure

Time: 10 minutes plus time for sharing

• Make a mind map to visualise the process of one of your projects.
  Be as detailed as you can regarding files needed and produced. Is external data required?

• How would you like to structure this project? Draw a management plan on a new piece of paper.
  Include files, folder structure, project structure and external resources required

• Put the two pieces of paper up for viewing by others.

Peer input

• Update your project and file structure based on the discussions.
• Start RStudio and make a new project, make sure that the check box for git is checked

Make directories in the Rstudio project

My take on a strategy

• Totally fine if you have another strategy,
  but remember that chaos does not count as a strategy!!

Project

• Good descriptive name of project, e.g ArcticMetatranscriptome
  
• Include information about the goal and reasoning for the project README

I always add the following directories/folders into the project directory:

• Data
  
• Analysis
  
• Docs
  
• Scripts
  
• Progs

Data

Read-only, raw data and meta data
This is an exact COPY of the data at the start of the project

Analysis

Make a separate folder for each of the steps in the analysis I like to number them to get a nice order

Docs

Put documentation (e.g Rmarkdown, Notes etc)

Scripts

Scripts, such as sbatch, bash, R scripts etc

Progs

Store software installed locally, also keep source code

How to succeed?

Think-Pair-Share
http://www.socrative.com
Student login, Room Name :AHREN

It is all about you!

• Find ways that work for you and stick to them
• Recognise your favourite excuse _ Resist the temptation of procrastination
  
• Move in small steps
  
• Set goals that are realistic

Use peer pressure (in a positive way)

• Share github repos!
• Meet and discuss your research projects
• Be the spearhead of change in your respective groups!

Conquer the FEAR!